Sequences associated with TDP-43 proteinopathies and methods of using the same

ABSTRACT

The present invention provides nucleic acids and peptides, and methods of using the nucleic acids and peptides to identify subjects at risk for a TDP-43 proteinopathy. The invention also provides for an array comprising the nucleic acids and peptides of the invention.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the priority of U.S. Ser. No. 14/514,104, filed Oct. 14, 2014, which claims the priority of U.S. Ser. No. 12/865,659, filed Nov. 22, 2010, which claims priority to PCT/US09/32627, filed Jan. 30, 2009, which claims priority to U.S. provisional application No. 61/025,377, filed Feb. 1, 2008, which is hereby incorporated by reference in its entirety.

GOVERNMENTAL RIGHTS

This invention was made with government support under P50-AG05681 awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD OF THE INVENTION

The present invention provides nucleic acid and amino acid sequences that may be utilized to identify subjects at risk for a TDP-43 proteinopathy.

BACKGROUND OF THE INVENTION

TAR DNA-binding protein 43 (TDP-43) is a pathological protein of sporadic and familial frontotemporal lobar degeneration (FTLD) with ubiquitin-positive, tau-negative inclusions (FTLD-U) with or without motor neuron disease (MND). MND is a neurodegenerative disorder involving the loss of upper and/or lower motor neurons and is characterized clinically by progressive weakness and death within a few years of onset; the most common clinical MND phenotype is amyotrophic lateral sclerosis (ALS). Recently, TAR DNA-binding protein 43 (TDP-43) was identified as a pathological protein of the motor neuron inclusions found in sporadic MND, but not in familial MND with Cu/Zn superoxide dismutase-1 (SOD1) mutation.¹⁻⁴ TDP-43 thus defines a class of neurodegenerative diseases referred to as TDP-43 proteinopathies. There is a need in the art for understanding the link between TDP-43 and these diseases, such that diagnostic and therapeutic treatments may be developed.

SUMMARY OF THE INVENTION

One aspect of the invention encompasses an isolated nucleic acid comprising at least ten contiguous nucleotides, including nucleotide 1077, of SEQ ID NO:1.

Another aspect of the invention encompasses an isolated peptide comprising at least ten contiguous amino acids, including amino acid 315, of SEQ ID NO:2.

Yet another aspect of the invention encompasses a method for identifying a subject at risk for a TDP-43 proteinopathy. The method comprises determining the identity of the nucleotide at position 1077 of a nucleotide sequence comprising the nucleic acid sequence of SEQ ID NO:1 in a sample from a subject. The presence of a G instead of an A at nucleotide 1077 indicates a risk for a TDP-43 proteinopathy.

An additional aspect of the invention encompasses a method for identifying a subject at risk for a TDP-43 proteinopathy. The method comprises determining the identity of the amino acid at position 315 of an amino acid sequence comprising the amino acid sequence of SEQ ID NO:2 in a sample from a subject. The presence of a threonine instead of an alanine at amino acid 315 indicates a risk for a TDP-43 proteinopathy.

A further aspect of the invention encompasses an array that comprises an address comprising an epitope binding agent. In one iteration, the epitope binding agent can specifically bind to SEQ ID NO:1 or a portion thereof containing nucleotide 1077. Alternatively, the epitope binding agent can specifically bind to SEQ ID NO:2 or a portion thereof containing amino acid 315.

Other aspects and iterations of the invention are described more thoroughly below.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A-C depicts illustrations showing that the missense mutation A315T within a highly conserved region of exon 6 of TDP-43 segregates with all affected members of an autosomal dominant MND family. (a) TDP-43 genomic structure, position of missense mutation, and location of amino acid change adjacent to glycine-rich domain. (b) Chromatogram of exon 6 displays a base pair change (c.1077 G>A) compared to family control. (c) Pedigree of family displays segregation of the mutation with disease (⋄=unaffected, ♦=affected with mutation, diagonal line=deceased). RsaI restriction digest was used to screen family members and 1,505 controls. Direct sequencing was also performed on all family members in this study to verify the mutation.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a nucleic acid sequence variant of TDP-43 (SEQ ID NO:1 in Table 1) that is associated with TDP-43 proteinopathies. In particular, nucleic acid 1077 of SEQ ID NO:1 is an A, as opposed to a G. Additionally, the invention provides an amino acid sequence variant (SEQ ID NO:2 in Table 1) of TDP-43 that is associated with TDP-43 proteinopathies. In particular, amino acid 315 of SEQ ID NO:2 is a threonine, as opposed to an alanine. The invention also encompasses methods of diagnosing or detecting a TDP-43 proteinopathy in a subject and an array. The sequences for SEQ ID Nos. 1, 2, 3, and 4 are shown in Table 1 below.

TABLE 1 SEQ ID ggtgggcggggggaggaggcggccctagcgccattttgtgggagcgaagcggtggctgggctgcgcttgggtccgtcgctgctt NO: 1 cggtgtccctgtcgggcttcccagcagcggcctagcgggaaaagtaaaagatgtctgaatatattcgggtaaccgaagatgaga acgatgagcccattgaaataccatcggaagacgatgggacggtgctgctctccacggttacagcccagtttccaggggcgtgtg ggcttcgctacaggaatccagtgtctcagtgtatgagaggtgtccggctggtagaaggaattctgcatgccccagatgctggctgg ggaaatctggtgtatgttgtcaactatccaaaagataacaaaagaaaaatggatgagacagatgcttcatcagcagtgaaagtg aaaagagcagtccagaaaacatccgatttaatagtgttgggtctcccatggaaaacaaccgaacaggacctgaaagagtatttt agtacctttggagaagttcttatggtgcaggtcaagaaagatcttaagactggtcattcaaaggggtttggctttgttcgttttacggaa tatgaaacacaagtgaaagtaatgtcacagcgacatatgatagatggacgatggtgtgactgcaaacttcctaattctaagcaaa gccaagatgagcctttgagaagcagaaaagtgtttgtggggcgctgtacagaggacatgactgaggatgagctgcgggagttct tctctcagtacggggatgtgatggatgtcttcatccccaagccattcagggcctttgcctttgttacatttgcagatgatcagattgcgc agtctctttgtggagaggacttgatcattaaaggaatcagcgttcatatatccaatgccgaacctaagcacaatagcaatagacag ttagaaagaagtggaagatttggtggtaatccaggtggctttgggaatcagggtggatttggtaatagcagagggggtggagctg gtttgggaaacaatcaaggtagtaatatgggtggtgggatgaactttggtacgttcagcattaatccagccatgatggctgccgccc aggcagcactacagagcagttggggtatgatgggcatgttagccagccagcagaaccagtcaggcccatcgggtaataacca aaaccaaggcaacatgcagagggagccaaaccaggccttcggttctggaaataactcttatagtggctctaattctggtgcagca attggttggggatcagcatccaatgcagggtcgggcagtggttttaatggaggctttggctcaagcatggattctaagtcttctggctg gggaatgtagacagtggggttgtggttggttggtatagaatggtgggaattcaaatttttctaaactcatggtaagtatattgtaaaata catatgtactaagaattttcaaaattggtttgttcagtgtggagtatattcagcagtatttttgacatttttctttagaaaaaggaagagcta aaggaattttataagttttgttacatgaaaggttgaaatattgagtggttgaaagtgaactgctgtttgcctgattggtaaaccaacaca ctacaattgatatcaaaaggtttctcctgtaatattttatccctggacttgtcaagtgaattctttgcatgttcaaaacggaaaccattgat tagaactacattctttaccccttgttttaatttgaaccccaccatatggatttttttccttaagaaaatctccttttaggagatcatggtgtca cagtgtttggttcttttgttttgttttttaacacttgtctcccctcatacacaaaagtacaatatgaagccttcatttaatctctgcagttcatct catttcaaatgtttatggaagaagcacttcattgaaagtagtgctgtaaatattctgccataggaatactgtctacatgctttctcattca agaattcgtcatcacgcatcacaggccgcgtctttgacggtgggtgtcccatttttatccgctactctttatttcatggagtcgtatcaac gctatgaacgcaaggctgtgatatggaaccagaaggctgtctgaacttttgaaaccttgtgtgggattgatggtggtgccgaggcat gaaaggctagtatgagcgagaaaaggagagagcgcgtgcagagacttggtggtgcataatggatattttttaacttggcgagatg tgtctctcaatcctgtggctttggtgagagagtgtgcagagagcaatgatagcaaataatgtacgaatgttttttgcattcaaaggac atccacatctgttggaagacttttaagtgagtttttgttcttagataacccacattagatgaatgtgttaagtgaaatgatacttgtactcc ccctacccctttgtcaactgctgtgaatgctgtatggtgtgtgttctcttctgttactgatatgtaagtgtggcaatgtgaactgaagctga tgggctgagaacatggactgagcttgtggtgtgctttgcaggaggacttgaagcagagttcaccagtgagctcaggtgtctcaaag aagggtggaagttctaatgtctgttagctacccataagaatgctgtttgctgcagttctgtgtcctgtgcttggatgctttttataagagttg tcattgttggaaattcttaaataaaactgatttaaataatatgtgtctttgttttgcagccctgaatgcaaagaattcatagcagttaattc cccttttttgacccttttgagatggaactttcataaagtttcttggcagtagtttattttgcttcaaataaacttatttgaaaagttgtctcaagt caaatggattcatcacctgtcatgcattgacacctgatacccagacttaattggtatttgttcttgcattggccaaagtgaaaattttttttt ttcttttgaaatctagttttgaataagtctgggtgaccgcacctaaaatggtaagcagtaccctccggctttttcttagtgcctctgtgcatt tgggtgatgttctatttacatggcctgtgtaaatctccattgggaagtcatgccttctaaaaagattcttatttgggggagtgggcaaaa tgttgattattttctaatgctttgtagcaaagcatatcaattgaaaagggaatatcagcaccttcctagtttgggatttgaaaagtggaat taattgcagtagggataaagtagaagaaaccacaaattatcttgtgcctgaaatccattaagaggcctgatagctttaagaattag ggtgggttgtctgtctggaagtgttaagtggaatgggctttgtcctccaggaggtgggggaatgtggtaacattgaatacagttgaat aaaatcgcttacaaaactcacactctcacaatgcattgttaagtatgtaaaagcaataacattgattctctgttgtacttttttgtaacta attctgtgagagttgagctcattttctagttggaagaatgtgatatttgttgtgttggtagtttacctaatgcccttacctaattagattatgat aaataggtttgtcattttgcaagttacataaacatttatcaatgaagtcatcctttagacttgtaatcgccacattgtttcattattcagtttc ctctgtaaagggatcttgagttgttttaattttttttttctgcatctgaatctgcatgatttccaaaccctgtaccatctgaattttgcattttagc acttgcactattactcagcagcagtaacatggtaacacttaaaatggtactcggggacctccaaagactaaactgacaagccttc aaggagcccaggggtaagttaacttgtcaacggcatggtttaatcccttctttacacttgtgtaaatttcagttactggtcatagaagg ctttcaatgttgagtggccttttattaacatgtttatggtactgcatagatacgggtatttattttaccctaagaagattttgaagtttaaaag tacttaaactatttggcaaagatttgtttttaaaaatctatttggtcaatctaaatgcattcattctaaaaaattttttgaaccagataaata aaatttttttttgacaccacaaaaaaaaaaaaaaaaaaaa SEQ ID MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILH NO: 2 APDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKE YFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQ SQDEPLRSRKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSL CGEDLIIKGISVHISNAEPKHNSNRQLERSGRFGGNPGGFGNQGGFGNSRGGGAGLGNNQ GSNMGGGMNFGTFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNM QREPNQAFGSGNNSYSGSNSGAAIGWGSASNAG SGSGFNGGFGSSMDSKSSGWGM SEQ ID ggtgggcggggggaggaggcggccctagcgccattttgtgggagcgaagcggtggctgggctgcgcttgggtccgtcgctgctt NO: 3 cggtgtccctgtcgggcttcccagcagcggcctagcgggaaaagtaaaagatgtctgaatatattcgggtaaccgaagatgaga acgatgagcccattgaaataccatcggaagacgatgggacggtgctgctctccacggttacagcccagtttccaggggcgtgtg ggcttcgctacaggaatccagtgtctcagtgtatgagaggtgtccggctggtagaaggaattctgcatgccccagatgctggctgg ggaaatctggtgtatgttgtcaactatccaaaagataacaaaagaaaaatggatgagacagatgcttcatcagcagtgaaagtg aaaagagcagtccagaaaacatccgatttaatagtgttgggtctcccatggaaaacaaccgaacaggacctgaaagagtatttt agtacctttggagaagttcttatggtgcaggtcaagaaagatcttaagactggtcattcaaaggggtttggctttgttcgttttacggaa tatgaaacacaagtgaaagtaatgtcacagcgacatatgatagatggacgatggtgtgactgcaaacttcctaattctaagcaaa gccaagatgagcctttgagaagcagaaaagtgtttgtggggcgctgtacagaggacatgactgaggatgagctgcgggagttct tctctcagtacggggatgtgatggatgtcttcatccccaagccattcagggcctttgcctttgttacatttgcagatgatcagattgcgc agtctctttgtggagaggacttgatcattaaaggaatcagcgttcatatatccaatgccgaacctaagcacaatagcaatagacag ttagaaagaagtggaagatttggtggtaatccaggtggctttgggaatcagggtggatttggtaatagcagagggggtggagctg gtttgggaaacaatcaaggtagtaatatgggtggtgggatgaactttggtgcgttcagcattaatccagccatgatggctgccgccc aggcagcactacagagcagttggggtatgatgggcatgttagccagccagcagaaccagtcaggcccatcgggtaataacca aaaccaaggcaacatgcagagggagccaaaccaggccttcggttctggaaataactcttatagtggctctaattctggtgcagca attggttggggatcagcatccaatgcagggtcgggcagtggttttaatggaggctttggctcaagcatggattctaagtcttctggctg gggaatgtagacagtggggttgtggttggttggtatagaatggtgggaattcaaatttttctaaactcatggtaagtatattgtaaaata catatgtactaagaattttcaaaattggtttgttcagtgtggagtatattcagcagtatttttgacatttttctttagaaaaaggaagagcta aaggaattttataagttttgttacatgaaaggttgaaatattgagtggttgaaagtgaactgctgtttgcctgattggtaaaccaacaca ctacaattgatatcaaaaggtttctcctgtaatattttatccctggacttgtcaagtgaattctttgcatgttcaaaacggaaaccattgat tagaactacattctttaccccttgttttaatttgaaccccaccatatggatttttttccttaagaaaatctccttttaggagatcatggtgtca cagtgtttggttcttttgttttgttttttaacacttgtctcccctcatacacaaaagtacaatatgaagccttcatttaatctctgcagttcatct catttcaaatgtttatggaagaagcacttcattgaaagtagtgctgtaaatattctgccataggaatactgtctacatgctttctcattca agaattcgtcatcacgcatcacaggccgcgtctttgacggtgggtgtcccatttttatccgctactctttatttcatggagtcgtatcaac gctatgaacgcaaggctgtgatatggaaccagaaggctgtctgaacttttgaaaccttgtgtgggattgatggtggtgccgaggcat gaaaggctagtatgagcgagaaaaggagagagcgcgtgcagagacttggtggtgcataatggatattttttaacttggcgagatg tgtctctcaatcctgtggctttggtgagagagtgtgcagagagcaatgatagcaaataatgtacgaatgttttttgcattcaaaggac atccacatctgttggaagacttttaagtgagtttttgttcttagataacccacattagatgaatgtgttaagtgaaatgatacttgtactcc ccctacccctttgtcaactgctgtgaatgctgtatggtgtgtgttctcttctgttactgatatgtaagtgtggcaatgtgaactgaagctga tgggctgagaacatggactgagcttgtggtgtgctttgcaggaggacttgaagcagagttcaccagtgagctcaggtgtctcaaag aagggtggaagttctaatgtctgttagctacccataagaatgctgtttgctgcagttctgtgtcctgtgcttggatgctttttataagagttg tcattgttggaaattcttaaataaaactgatttaaataatatgtgtctttgttttgcagccctgaatgcaaagaattcatagcagttaattc cccttttttgacccttttgagatggaactttcataaagtttcttggcagtagtttattttgcttcaaataaacttatttgaaaagttgtctcaagt caaatggattcatcacctgtcatgcattgacacctgatacccagacttaattggtatttgttcttgcattggccaaagtgaaaattttttttt ttcttttgaaatctagttttgaataagtctgggtgaccgcacctaaaatggtaagcagtaccctccggctttttcttagtgcctctgtgcatt tgggtgatgttctatttacatggcctgtgtaaatctccattgggaagtcatgccttctaaaaagattcttatttgggggagtgggcaaaa tgttgattattttctaatgctttgtagcaaagcatatcaattgaaaagggaatatcagcaccttcctagtttgggatttgaaaagtggaat taattgcagtagggataaagtagaagaaaccacaaattatcttgtgcctgaaatccattaagaggcctgatagctttaagaattag ggtgggttgtctgtctggaagtgttaagtggaatgggctttgtcctccaggaggtgggggaatgtggtaacattgaatacagttgaat aaaatcgcttacaaaactcacactctcacaatgcattgttaagtatgtaaaagcaataacattgattctctgttgtacttttttgtaacta attctgtgagagttgagctcattttctagttggaagaatgtgatatttgttgtgttggtagtttacctaatgcccttacctaattagattatgat aaataggtttgtcattttgcaagttacataaacatttatcaatgaagtcatcctttagacttgtaatcgccacattgtttcattattcagtttc ctctgtaaagggatcttgagttgttttaattttttttttctgcatctgaatctgcatgatttccaaaccctgtaccatctgaattttgcattttagc acttgcactattactcagcagcagtaacatggtaacacttaaaatggtactcggggacctccaaagactaaactgacaagccttc aaggagcccaggggtaagttaacttgtcaacggcatggtttaatcccttctttacacttgtgtaaatttcagttactggtcatagaagg ctttcaatgttgagtggccttttattaacatgtttatggtactgcatagatacgggtatttattttaccctaagaagattttgaagtttaaaag tacttaaactatttggcaaagatttgtttttaaaaatctatttggtcaatctaaatgcattcattctaaaaaattttttgaaccagataaata aaatttttttttgacaccacaaaaaaaaaaaaaaaaaaaa SEQ ID MSEYIRVTEDENDEPIEIPSEDDGTVLLSTVTAQFPGACGLRYRNPVSQCMRGVRLVEGILH NO: 4 APDAGWGNLVYVVNYPKDNKRKMDETDASSAVKVKRAVQKTSDLIVLGLPWKTTEQDLKE YFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQ SQDEPLRSRKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSL CGEDLIIKGISVHISNAEPKHNSNRQLERSGRFGGNPGGFGNQGGFGNSRGGGAGLGNNQ GSNMGGGMNFGAFSINPAMMAAAQAALQSSWGMMGMLASQQNQSGPSGNNQNQGNM QREPNQAFGSGNNSYSGSNSGAAIGWGSASNAGSGSGFNGGFGSSMDSKSSGWGM I. Nucleic Acid

One aspect of the present invention encompasses an isolated nucleic acid. Generally speaking, the sequence of the nucleic acid comprises nucleotide position 1077 of SEQ ID NO:1. In particular, the sequence of the nucleic acid comprises an A at position 1077 of SEQ ID NO:1, as opposed to the wild-type sequence that has a G at position 1077 (SEQ ID NO:3, Table 1). In one embodiment, the nucleic acid comprises at least five contiguous nucleotides, including nucleotide 1077, of SEQ ID NO:1. In another embodiment, the nucleic acid comprises at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, or at least 100 contiguous nucleotides, including nucleotide 1077, of SEQ ID NO:1. In yet another embodiment, the nucleic acid comprises at least 200, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, or at least 1000 contiguous nucleotides, including nucleotide 1077, of SEQ ID NO:1. In a further embodiment, the nucleic acid comprises at least 1000, at least 2000, at least 3000, at least 4000, or more than 4000 contiguous nucleotides, including nucleotide 1077, of SEQ ID NO:1.

In an alternative embodiment, the nucleic acid comprises exon 6 of TDP-43, wherein nucleic acid 1077 is an A instead of a G. In another alternative embodiment, the nucleic acid comprises the cDNA of TDP-43, wherein nucleic acid 1077 is an A instead of a G. In certain embodiments, the nucleic acid consists of the nucleic acid sequence of SEQ ID NO:1.

The present invention also encompasses nucleic acids that are complementary to the isolated nucleic acid sequences described above. For instance, in some embodiments, a nucleic acid of the invention hybridizes to a nucleic acid comprising nucleotide position 1077 of SEQ ID NO:1. In other embodiments, the nucleic acid hybridizes to a nucleic acid comprising nucleotide 1077 of SEQ ID NO:1 but not to a nucleic acid comprising nucleotide 1077 of SEQ ID NO:3. In one embodiment, the nucleic acid hybridizes to a nucleic acid comprising exon 6 of TDP-43, wherein nucleic acid 1077 is an A instead of a G.

Hybridization of nucleic acids is typically performed under stringent conditions. Nucleic acid duplex or hybrid stability is expressed as the melting temperature or Tm, which is the temperature at which a probe dissociates from a target DNA. This melting temperature is used to define the required stringency conditions. To maximize the rate of annealing of the probe with its target, hybridizations are generally carried out at a temperature that is about 20 to 25° C. below the Tm. For instance, stringent conditions may typically involve hybridizing at about 68° C. in 5×SSC/5×Denhardt's solution/1.0% SDS, and washing in 0.2×SSC/0.1% SDS at about 68° C. Moderately stringent conditions include washing in 3×SSC at 42° C. The parameters of salt concentration and temperature can be varied to achieve the optimal level of identity between the nucleic acid and the target sequence, for instance, a sequence comprising nucleotide 1077 of SEQ ID NO:1. One skilled in the art will appreciate which parameters to manipulate to optimize hybridization. Additional guidance regarding such conditions is readily available in the art, for example, by Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, N.Y.; and Ausubel et al., (eds.), 1995, Current Protocols in Molecular Biology, (John Wiley & Sons, N.Y.) at Unit 2.10.

The isolated nucleic acids of the invention may be labeled. Non-limiting examples of suitable labels may include fluorescent labels, chemiluminescent labels, radioactive labels, colorimetric labels, and resonance labels. Methods of labeling nucleic acids are well known in the art.

The various nucleic acids mentioned above may be obtained using a variety of different techniques known in the art. The nucleic acids may be isolated using standard techniques, may be synthesized using standard techniques, or may be purchased or obtained from a depository. Once the nucleic acid is obtained, it may be amplified and/or sequenced for use in a variety of applications, e.g. the methods described below.

The invention also encompasses production of nucleic acids comprising nucleotide 1077 of SEQ ID NO:1, or derivatives or fragments thereof, that may be made by any method known in the art, including by synthetic chemistry. After production, the synthetic sequence may be inserted into any of the many available expression vectors and cell systems using reagents well known in the art.

II. Peptide

Another aspect of the present invention encompasses an isolated peptide. Generally speaking, the amino acid sequence of the peptide comprises the amino acid at position 315 of SEQ ID NO:2. In particular, the sequence of the peptide comprises threonine at position 315 of SEQ ID NO:2, as opposed to the wild-type sequence that has an alanine at position 315 (SEQ ID NO:4 in Table 1). In one embodiment, the peptide comprises at least five contiguous amino acids, including amino acid 315, of SEQ ID NO:2. In another embodiment, the peptide comprises at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 90 or at least 100 contiguous amino acids, including amino acid 315, of SEQ ID NO:2. In yet another embodiment, the peptide comprises at least 200, at least 300, at least 400 or at least 500 contiguous amino acids, including amino acid 315, of SEQ ID NO:2.

In an alternative embodiment, the peptide comprises the translated amino acid sequence of exon 6 of TDP-43, wherein amino acid 315 is a threonine. In yet another alternative, the peptide consists of the amino acid sequence of TDP-43, wherein amino acid 315 is a threonine.

The isolated peptide of the invention may be labeled. Non-limiting examples of suitable labels include fluorescent labels, chemiluminescent labels, radioactive labels, colorimetric labels, and resonance labels. Methods of labeling peptides are well known in the art.

The various peptides mentioned above may be obtained using a variety of different techniques known in the art. The peptides may be isolated using standard techniques, may be synthesized using standard techniques, or may be purchased or obtained from a depository.

The invention also encompasses production of peptides comprising amino acid 315 of SEQ ID NO:2, or derivatives or fragments thereof, that may be made by any method known in the art, including by synthetic chemistry.

III. Methods

Yet another aspect of the invention encompasses methods for determining risk and diagnosis of a TDP-43 proteinopathy. As used herein, a TDP-43 proteinopathy is a disorder or a disease characterized in part by a mutation or malfunction of the TDP-43 protein. In an exemplary embodiment, a TDP-43 proteinopathy is a disease or a disorder characterized in part by the substitution of the guanine at nucleotide 1077 of SEQ ID NO:3 to an adenine resulting in the nucleic acid sequence variant of SEQ ID NO:1, or the substitution of the alanine at amino acid 315 of SEQ ID NO:4 to a threonine resulting in the amino acid sequence variant of SEQ ID NO:2. Non-limiting examples of a TDP-43 proteinopathy may include sporadic frontotemporal lobar degeneration (FTLD), also called frontotemporal dementia, familial FTLD, sporadic MND, familial MND, sporadic ALS, and familial ALS, and combinations of these two motor and cognitive phenotypes, including FTLD-MND.

In one embodiment, the invention provides a method for determining whether a subject is at risk for a TDP-43 proteinopathy. For instance, in some embodiments, the invention provides a method for determining whether a subject is at risk for ALS. Generally speaking, the method comprises determining whether the subject has an adenine at nucleotide 1077 of TDP-43 instead of a guanine. If an adenine is present, the subject may be at risk for developing a TDP-43 proteinopathy. Alternatively, the method may comprise determining whether the subject has a threonine at amino acid 315 of TDP-43 instead of an alanine. If a threonine is present, the subject may be at risk for developing a TDP-43 proteinopathy.

In another embodiment, the invention provides a method for diagnosing a subject with a TDP-43 proteinopathy. For instance, in some embodiments, the invention provides a method for diagnosing a subject with ALS. Typically, the method comprises determining whether the subject has an adenine at nucleotide 1077 of TDP-43 instead of a guanine. If an adenine is present, the subject may be diagnosed with a TDP-43 proteinopathy. Alternatively, the method may comprise determining whether the subject has a threonine at amino acid 315 of TDP-43 instead of an alanine. If a threonine is present, the subject may be diagnosed with a TDP-43 proteinopathy.

Methods for determining whether a subject has an adenine at nucleotide 1077 of TDP-43 instead of a guanine are known in the art. For instance, sequencing of a portion of TDP-43 encompassing nucleotide 1077 may be performed as detailed in the examples. Alternatively, an array may be used as detailed below.

In certain embodiments, nucleic acid from a subject may be digested with a restriction enzyme that generates a unique fragment in a subject with an adenine at nucleotide 1077 of TDP-43 instead of a guanine. For instance, the restriction enzyme Rsa1 may be used. Rsa1 generates a unique fragment when incubated with a nucleic acid comprising exon 6 of TDP-43 when nucleotide 1077 is an adenine. The fragment may be amplified from genomic DNA using the polymerase chain reaction method. For instance, see FIG. 1C.

Similarly, methods for determining whether a subject has a threonine at amino acid 315 of TDP-43 instead of an alanine are known in the art. For instance, an array may be used as detailed below. Alternatively an antibody that recognizes a threonine at position 315, but not an alanine, may be used.

Methods of obtaining a nucleic acid and/or a peptide of the invention from a subject are known in the art. For instance, biological samples comprising a nucleic acid and/or a peptide of the invention may be collected from a subject. Non-limiting examples of suitable biological samples may include blood samples, tissues samples, or bodily fluid samples. Blood samples may include whole blood, serum, or plasma. Bodily fluid samples may include urine, lymph, or saliva samples.

Suitable subjects express TDP-43. For instance, humans, non-human primates, rodents, livestock animals, and companion animals are non-limiting examples of suitable subjects. Rodents may include mice, rats, and guinea pigs. Livestock animals may include cattle, swine, and chicken. Companion animals may include cats and dogs. In some embodiments, the subject is a frog. In each of the above embodiments, the subject may have a family history of a TDP-43 proteinopathy, of a MND, or of FTLD. Alternatively, the subject may have symptoms of a TDP-43 proteinopathy, of a MND, or of a FTLD. In some embodiments, the subject may have no clinical symptoms of a TDP-43 proteinopathy, of a MND, or of a FTLD.

IV. Array

A further aspect of the invention is an array comprising at least one address. In some embodiments, at least one address of the array has disposed thereon an epitope binding agent that can specifically bind to SEQ ID NO:1, or a portion thereof, containing nucleotide 1077. In other embodiments, at least one address of the array has disposed thereon an epitope binding agent that can specifically bind to SEQ ID NO: 2, or a portion thereof, containing amino acid 315.

Several substrates suitable for the construction of arrays are known in the art, and one skilled in the art will appreciate that other substrates may become available as the art progresses. The substrate may be a material that may be modified to contain discrete individual sites appropriate for the attachment or association of an epitope binding agent and is amenable to at least one detection method. Non-limiting examples of substrate materials include glass, modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, TeflonJ, etc.), nylon or nitrocellulose, polysaccharides, nylon, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses and plastics. In an exemplary embodiment, the substrate may allow optical detection without appreciably fluorescing.

A substrate may be planar, a substrate may be a well, i.e. a 364 well plate, or alternatively, a substrate may be a bead. Additionally, the substrate may be the inner surface of a tube for flow-through sample analysis to minimize sample volume. Similarly, the substrate may be flexible, such as a flexible foam, including closed cell foams made of particular plastics.

An epitope binding agent may be attached to the substrate in a wide variety of ways, as will be appreciated by those in the art. The nucleic acid or epitope binding agent may either be synthesized first, with subsequent attachment to the substrate, or may be directly synthesized on the substrate. The substrate and the epitope binding agent may be derivatized with chemical functional groups for subsequent attachment of the two. For example, the substrate may be derivatized with a chemical functional group including, but not limited to, amino groups, carboxyl groups, oxo groups or thiol groups. Using these functional groups, the epitope binding agent may be attached using functional groups on the nucleic acid or epitope binding agent either directly or indirectly using linkers.

The epitope binding agent may also be attached to the substrate non-covalently. For example, a biotinylated epitope binding agent may be prepared, which may bind to surfaces covalently coated with streptavidin, resulting in attachment. Alternatively, an epitope binding agent may be synthesized on the surface using techniques such as photopolymerization and photolithography. Additional methods of attaching epitope binding agents to arrays and methods of synthesizing biomolecules on substrates are well known in the art, i.e. VLSIPS technology from Affymetrix (e.g., see U.S. Pat. No. 6,566,495, and Rockett and Dix, Xenobiotica 30(2):155-177, both of which are hereby incorporated by reference in their entirety).

In one embodiment, the epitope binding agent attached to the substrate is located at a spatially defined address of the array. Arrays may comprise from about 1 to about several hundred thousand addresses. In one embodiment, the array may be comprised of less than 10,000 addresses. In another alternative embodiment, the array may be comprised of at least 10,000 addresses. In yet another alternative embodiment, the array may be comprised of less than 5,000 addresses. In still another alternative embodiment, the array may be comprised of at least 5,000 addresses. In a further embodiment, the array may be comprised of less than 500 addresses. In yet a further embodiment, the array may be comprised of at least 500 addresses.

An epitope binding agent may be represented more than once on a given array. In other words, more than one address of an array may be comprised of the same epitope binding agent. In some embodiments, two, three, or more than three addresses of the array may be comprised of the same epitope binding agent. In certain embodiments, the array may comprise control epitope binding agents and/or control addresses. The controls may be internal controls, positive controls, negative controls, or background controls.

As used herein, “epitope binding agent” may refer to a nucleic acid, an oligonucleic acid, an amino acid, a peptide, a polypeptide, a protein, a lipid, a metabolite, a small molecule or a fragment thereof that recognizes and is capable of binding to SEQ ID NO: 2 or a portion thereof containing amino acid 315, or to SEQ ID NO:1 or a portion thereof containing nucleic acid 1077. Nucleic acids may include RNA, DNA, and naturally occurring or synthetically created derivatives.

In further embodiments, an epitope binding agent of the array may recognize mutations in one or more of the sequences selected from the group of sequences comprising the vesicle-associated membrane protein-associated protein B (VAPB), dynactin (DCTN1), alsin (ALS2), immunoglobulin μ binding protein 2 (IGHMBP2), or glycyl-tRNA synthetase (GARS) genes that are associated with MND.

The arrays may be utilized in several suitable applications. For example, the arrays may be used in methods for detecting association between an epitope binding agent and a target. As used herein, “target” refers to a nucleic acid comprising nucleotide 1077 of SEQ ID NO:1 or a peptide comprising amino acid 315 of SEQ ID NO:2. This method typically comprises incubating a sample comprising a target with the array under conditions such that the target may associate with the epitope binding agent attached to the array. The association may then be detected, using means commonly known in the art, such as fluorescence. “Association,” as used in this context, may refer to hybridization, covalent binding, or ionic binding. A skilled artisan will appreciate that conditions under which association may occur will vary depending on the epitope binding agent, the substrate, the sample, and the detection method utilized. As such, suitable conditions may have to be optimized for each individual array created.

In yet another embodiment, the array may be used as a tool in a method for determining whether a subject is at risk for developing a TDP-43 proteinopathy. Similarly, the array may be used as a tool in a method for determining whether a subject is at risk for a MND. Alternatively, the array may be used as a tool in a method for determining whether a subject is at risk for ALS. In another alternative, the array may be used as a tool in a method for determining whether a subject is at risk for FTLD. Typically, such a method comprises incubating the array with a biological sample from the subject. If the biological sample comprises a nucleic acid comprising nucleotide 1077 of SEQ ID NO:1, or a peptide comprising amino acid 315 of SEQ ID NO:2, then an association between the array and the sample may be detected, and the subject may be at risk for developing a TDP-43 proteinopathy.

In certain embodiments, the array may be used as a tool in a method for diagnosing a subject with a TDP-43 proteinopathy. Similarly, the array may be used as a tool in a method for diagnosing a subject with a MND. Alternatively, the array may be used as a tool in a method for diagnosing a subject with ALS. In another alternative, the array may be used as a tool in a method for diagnosing a subject with a FTLD. Typically, such a method comprises incubating the array with a biological sample from the subject. If the biological sample comprises a nucleic acid comprising nucleotide 1077 of SEQ ID NO:1, or a peptide comprising amino acid 315 of SEQ ID NO:2, then an association between the array and the sample may be detected, and the subject may be diagnosed with a TDP-43 proteinopathy.

In each of the above embodiments, the subject may not display clinical signs of MND, ALS, or FTLD. In some embodiments, the subject may display only a few clinical signs of MND, ALS or FTLD.

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventors to function well in the practice of the invention. Those of skill in the art should, however, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention, therefore all matter set forth or shown in the accompanying drawings is to be interpreted as illustrative and not in a limiting sense.

EXAMPLES

The following examples illustrate various iterations of the invention.

Methods

Genetic analysis. High molecular weight DNA was extracted from whole blood, serum or brain tissue according to standard procedures. DNA from serum was whole-genome amplified using the REPLI-g® Midi Kit (Qiagen Inc., Valencia, Calif., USA) prior to genetic analysis. DNA from a single affected individual from each family was used for sequencing of TDP-43. All exons and the intron-exon boundaries of the TDP-43 gene were amplified using gene specific intronic primers. Direct sequencing of the amplified fragments was performed using the Big Dye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems, Wellesley, Mass., USA) and standard protocols. For most of the fragments the primers used for sequencing were the same as those used for PCR amplification. Reactions were run on an ABI3130 and mutation analysis was performed using Sequencher software v4.6 (Gene Codes Corporation, Ann Arbor, Mich., USA). Positive calls for sequence variants were made only if the variant was observed in both forward and reverse sequence reads. Where possible, sequence variants were tested for segregation with the disease and screened in a set of 1,505 unrelated ethnically-matched controls.

Example 1: Screening

Mutation analysis of the TDP-43 gene was undertaken in 8 families with MND/ALS with an autosomal dominant pattern of inheritance and no mutation within the SOD1 gene, 5 families with familial FTLD-MND, and 25 families with FTLD-U.¹⁴ All families were of European descent. No sporadic cases of MND were available, but additional sporadic cases of FTLD-MND (n=6) and FTLD-U (n=28) were investigated.

This analysis led to the identification of a missense mutation, Ala-315-Thr (c.1077G>A) within exon 6. In TDP-43 this alanine residue is highly conserved throughout the evolutionary spectrum from Homo sapiens to Xenopus tropicalis, supporting its likely functional importance (Table 2). The A315T mutation segregated with all affected members of an autosomal dominant MND family (additional non-coding sequence variants were also identified in cases with FTLD-U, FTLD-MND, and MND see FIGS. 1b & c and Table 3). This mutation was absent from a large series of ethnically matched elderly controls (n=1,505).

The phenotype of the four affected family members with the TDP-43 A315T mutation involved a slowly progressive lower motor neuron degeneration syndrome with respiratory involvement, with only minimal involvement of upper motor or bulbar neurons and absence of dementia (Table 3). Brain autopsy in this kindred remains to be undertaken. Similar clinical phenotypes have been reported in sporadic MND and in kindreds with SOD1 mutations.^(5,6) The TDP-43 mutation in familial MND reported here supplements other familial neurodegenerative conditions that affect predominantly lower motor neurons including mutations in the vesicle-associated membrane protein-associated protein B (VAPB), dynactin (DCTN1), alsin (ALS2), immunoglobulin μ binding protein 2 (IGHMBP2), and glycyl-tRNA synthetase (GARS) genes, and other mutations in juvenile MND, although some of these mutations have been identified in motor neuron diseases and hereditary motor neuropathies with variable clinical phenotypes.¹⁵

These data have important implications for both sporadic and familial forms of MND and FTLD-U, which are linked by a common molecular pathology: TDP-43 proteinopathy. The discovery of a missense mutation in TDP-43 in a family with dominantly inherited MND provides evidence of a direct link between TDP-43 function and neurodegeneration.

Example 2: Clinical Family Analysis

The proband (subject III-1 of FIG. 1d )) developed weakness and atrophy of his right hand at age 48 years. Leg strength, mental status, cranial nerves, sensory examination, reflexes, coordination and gait were normal at initial examination; upper motor neuron findings were absent. Motor and sensory nerve conduction was normal, but electromyography (EMG) showed denervation in the arms both proximally and distally, with fasciculation potentials in the legs, and occasional large motor unit potentials. Magnetic resonance imaging (MRI) of brain and spinal cord were normal, as was blood work including absent anti-GM1 antibodies; SOD1 gene testing was normal. Three years later his upper extremity weakness had progressed but mental status, cranial nerve function, leg strength, and sensation remained normal.

The proband's father (subject II-2) developed a left foot drop at age 72. Exam showed atrophy and distal weakness in the left foot, fasciculations, and increased deep tendon reflexes without other abnormalities. EMG revealed widespread fasciculations with denervation changes in the legs and paraspinous muscles. Weakness steadily progressed to involve all four extremities with respiratory and swallowing difficulty, and he died of respiratory compromise seven years after diagnosis.

Subject II-3 developed left foot drop at age 64, which progressed to involve both legs and his arms within two years. Examination at age 69 showed symmetric proximal and distal weakness in the upper extremities, with asymmetric (left>right) distal predominant weakness in the legs. Reflexes were brisk throughout. Electrophysiology showed normal sensory and motor nerve conduction, with denervation changes in both the upper and lower extremities. Respiratory weakness developed at age 72 years, and he died of respiratory complications at age 73 years.

Subject II-4 developed right leg weakness at age 83, which progressed to involve both legs requiring wheelchair dependence within two years. Asymmetric arm weakness and respiratory weakness developed at age 85 and at age 86 there was severe atrophy and weakness in the lower and upper extremities with widespread fasciculations.

For more details, see Table 4.

TABLE 2 TDP-43 protein (291-340 amino acids) displays high similarity between species. Residues underlined indicate differences when compared to humans. TDP-43 A315T location is indicated in bold italic. SEQ. ID Species 291-340 NO. Homo NSRGGGAGLGNNQGSNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML  5 sapiens Pan NSRGGGAGLGNNQGSNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML  6 troglodytes Macaca NSRGGGAGLGNNQGSNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML  7 mulatta Bos Taurus NSRGGGAGLGNNQGSNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML  8 Felis catus NSRGGGAGLGNNQGSNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML  9 Cavia N-RGGGAGLGNNQGSNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML 10 porcellus Rattus NSRGGGAGLGNNQGGNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML 11 norvegicus Mus NSRGGGAGLGNNQGGNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML 12 musculus Gallus NSRGGGGGLGNNQGSNM--GGGMNFG

FSINPAMMAAAQAALQSSWGMMGML 13 gallus Xenopus NSRPSSGALGNNQGGNMGGGGGMNFG

FSINPAMMAAAQAALQSSWGMMGML 14 tropicalis

TABLE 3 Nucleotide Amino Pathological Position Region change acid entities Frequency c.1-430 5′UTR G > A n/a MND 0.04a c.332 Ex 2 T > C A 66 A MND, FTLD- 0.01087b MND, control c.848 + 69 In 5-6 {grave over ( )}+/G n/a MND, FTLD- 0.25c MND, FTLD-U, control c.1077 Ex 6 G > A A 315 T MND 0.0003d c.2076 3′UTR G > A n/a MND, FTLD-U 0.0072e c.3674 3′UTR +/GTTTT n/a MND, FTLD- 0.8409f MND, FTLD-U, control (numbering corresponds to polymorphism location with respect to NM_007375); Frequency based on number of chromosomes screened (a) 60/1, 390, (b) 3/276, (c) 19/76, (d) 1/3, 010, (e) 2/276, (f) 37/44). With 276 chromosomes screened and a population frequency of 1%, the power to detect a variant is 0.94.

TABLE 4 Clinical features of a family with MND with a TDP-43 A315T variant. Electrophysiology Age at Nerve onset/ Clinical findings conductions death Mental Cranial Respiratory Site of Disease (age Subject (years) status nerves involvement onset course performed) Electromyography II-2 72/79 Normal Normal Yes Left Progressive Normal Fibs/PSW lower asymmetric SNAP in legs, extremity lower motor amplitudes, thoracic neuron loss normal paraspinous in legs sensory and muscles. before motor Reduced arms, distal velocities recruitment. before (72) Occasional proximal. large motor Brisk units. reflexes. Fasciculations Death from throughout. respiratory weakness. II-3 64/74 Normal Normal Yes Left Progressive Normal Fibs/PSW lower asymmetric SNAP in legs and extremity lower motor amplitudes, arms. neuron loss normal Reduced in legs sensory and recruitment. before motor Occasional arms, distal velocities large motor and (68) units. proximal. Fasciculations Brisk throughout. reflexes. Death from respiratory weakness. II-4 83 Normal Normal Yes Right Progressive Not available Not lower asymmetric available extremity lower motor neuron loss, distal and proximal, legs before arms. Brisk reflexes. III-1 48 Normal Normal No Right Progressive Normal Fibs/PSW upper asymmetric SNAP in arms. extremity lower motor amplitudes, Fasciculations neuron normal in arms/legs loss, distal sensory and before motor proximal, velocities arms (49) before legs. Fibs = fibrillations; PSW = positive sharp waves; SNAP = sensory nerve action potential.

REFERENCES

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What is claimed is:
 1. An oligonucleotide probe comprising a fragment of a TAR DNA-binding protein 43 (TDP-43) nucleotide sequence or a complement of the TDP-43 nucleotide sequence, wherein the fragment comprises fifteen to 200 contiguous nucleotides of (i) the TDP-43 nucleotide sequence of SEQ ID NO: 1 that includes nucleotide position 1077, wherein the fragment has an A at a position corresponding to nucleotide position 1077 of SEQ ID NO:1, or (ii) a sequence that is complementary to the TDP-43 nucleotide sequence of SEQ ID NO: 1 that includes nucleotide position 1077, wherein the fragment has a T at a position corresponding to nucleotide position 1077 of SEQ ID NO:1, and wherein the oligonucleotide probe is detectably labeled with a fluorescent, chemiluminescent, radioactive, colorimetric, and/or resonance label.
 2. The oligonucleotide probe of claim 1, wherein the probe comprises between 15 and 50 nucleotides.
 3. An array comprising a substrate, wherein the substrate comprises the oligonucleotide probe of claim
 1. 